QC Metrics Summary



This QC Metrics Summary puts together the QC metrics returned by the Cell Ranger pipeline with multiomics, single cell or bulk sequencing data. It helps the user visualize the distribution of the QC metrics, helping identify outliers and batch effects. It also proposes different outlier detection methods.

Outlier Detection

Sample ID Alerts Outliers with Z-Score Outliers with Dixon Q Test Outliers with LOF
14 0 3 ( 1 Joint 2 ATAC ) 4 ( 1 Joint 3 ATAC ) Outlier
5 3 0 0 0
3 3 0 0 0
10 0 1 ( 1 ATAC ) 1 ( 1 ATAC ) 0
9 3 0 0 0
6 2 1 ( 1 GEX ) 1 ( 1 GEX ) 0
12 2 0 1 ( 1 ATAC ) 0
11 2 2 ( 2 Joint ) 1 ( 1 Joint ) Outlier
8 3 0 0 0
2 1 2 ( 1 Joint 1 ATAC ) 1 ( 1 Joint ) Outlier
7 1 0 0 0
13 0 0 0 0
4 0 1 ( 1 GEX ) 1 ( 1 GEX ) 0
A 2 0 2 ( 2 ATAC ) 0

QC Metrics Table

Violin Plot

Principal Component Analysis

Clustermap